Program gto_fasta_extract_by_read

The gto_fasta_extract_by_read extracts sequences from a FASTA or Multi-FASTA file, which the range is defined by the user in the parameters.

For help type:


			  			./gto_fasta_extract_by_read -h

In the following subsections, we explain the input and output paramters.

Input parameters

The gto_fasta_extract_by_read program needs two paramenters, which defines the begin and the end of the extraction, and two streams for the computation, namely the input and output standard. The input stream is a FASTA or Multi-FASTA file.

The attribution is given according to:


			  			Usage: ./gto_fasta_extract_by_read [options] [[--] args]
or: ./gto_fasta_extract_by_read [options]

It extracts sequences from each read in a Multi-FASTA file (splited by \n)

-h, --help            show this help message and exit

Basic options
-i, --init=      The first position to start the extraction (default 0)
-e, --end=       The last extract position (default 100)
< input.fasta         Input FASTA or Multi-FASTA file format (stdin)
> output.fasta        Output FASTA or Multi-FASTA file format (stdout)

Example: ./gto_fasta_extract_by_read -i  -e  < input.mfasta > output.mfasta

An example of such an input file is:


			  			>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCCC
GGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAA
GTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGTGCC
GCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCCCAGC
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGT
GGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTG
GTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAG
GCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAA
TAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA

Output

The output of the gto_fasta_extract_by_read program is FASTA or Multi-FASTA file wiht the extracted sequences.

Using the input above with the value 0 as the extraction starting point and the 50 as the ending, an output example for this is the following:


			  			>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGG
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCC